That Gibbs & Ellie scene was Bishop's way of asking for permission in a way... Or at least waiting for Gibbs to say 'no'... I think Gibbs saw it coming, but also thought that Ellie needed to find her way, and figure out whether she wants to be a CIA agent/deep undercover agent or not... As he said to McGee "Bishop was at crossroads"...
The Ellick scene was heartbreaking yes, but it also left things open enough...
And I think Ellie just wanted to cut ties as quickly as possible, because she knew that otherwise she would never leave...